Big Thunder Mountain began as an idea for a ride to replace Pirates of the Caribbean at Walt Disney World. Because Walt Disney World was too close to the original New Orleans it was decided not to build New Orleans Square there as it had been built at Disneyland. This meant that they would not get the famed "Pirates of the Caribbean" attraction from Disneyland.

A Team of Imagineers led by Marc Davis created a new area for Walt Disney World with the theme of an old west town. The area would be called Thunder Mesa and feature an animatronic show like ‘Pirates of the Caribbean" called "The Western River Expedition" and a run-a-way mine train ride that would sit on top of a mesa (Thunder Mesa). Using Marc Davis’ sketches, Imagineer Tony Baxter was given the task of creating the models for the run-a-way mine-train of Thunder Mesa.

When it was decided that Pirates of the Caribbean would in fact be built at Disneyworld after all, the mine train project was slated to open by itself. Years went by however and nothing got built. Back at Disneyland however, WED Imagineers devised what they called "The Disneyland Master Plan". This plan laid out future projects for Disneyland in the years to come and included plans for the expansion of New Orleans Square and Main Street, along with Tony Baxter’s proposed Discovery Bay area. Disneyland needed a new thrill ride to mark the new entrance of these areas. This is finally where the Mine Train idea would come to fruition.

Baxter’s original model for Thunder Mesa was scaled back to fit the more intimate theme and size constraints at Disneyland. As the design moved away from the original mesa concept and into a theme based on Monument Valley, the name of the attraction was officially changed from Thunder Mesa to Big Thunder. Later the Monument Valley theme would give way to the Bryce Canyon motif we see today. It was decided that the rockwork of Bryce Canyon better matched the fantasy inspired themes of Frontierland and Fantasyland, and also melded well with the pine and aspen trees surrounding the area.

As the attraction was plotting on storyboards a story developed. Greedy prospectors were plundering the hills of Big Thunder, once sacred Indian ground, for their gold. Indian legend warned of a great disaster that would befall anyone who disturbed the mountain. One night the miners set out on the train down into the deep mines of the mountain. Here, Indian spirits took control of the mine train and set it out of control down the mountain, and the miners were never seen again. Later a great earthquake would destroy much of the mine and as more disasters occurred the frightened miners fled from Big Thunder leaving only a handful of residents and of course the legend of Big Thunder.